mapDamage

bioconda installation

• python3 version 2.2.1

conda install -c bioconda mapdamage2=2.2.1

• python3 version 2.2.1 with R and 4 mandatory packages for the Bayesian inference:

conda install -c bioconda mapdamage2=2.2.1=pyr40_0

Important

• From version 2.2.1 the master branch is requiring python3 as python2 is not supported from 2020-01-01.

Introduction

Complete documentation, instructions, examples, screenshots and FAQ are available at this address.

mapDamage2 is a computational framework written in Python3 and R, which tracks and quantifies DNA damage patternsamong ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.

mapDamage was developed at the Centre for GeoGenetics by the Orlando Group .

Citation

If you use this program, please cite the following publication:Jónsson H, Ginolhac A, Schubert M, Johnson P, Orlando L.mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters.Bioinformatics 23rd April 2013. doi: 10.1093/bioinformatics/btt193

The original mapDamage1 was published in the following article:Ginolhac A, Rasmussen M, Gilbert MT, Willerslev E, Orlando L.mapDamage: testing for damage patterns in ancient DNA sequences. Bioinformatics 2011 27(15):2153-5http://bioinformatics.oxfordjournals.org/content/27/15/2153

Test the no-stats part and rescaling

you can test mapDamage by running:

cd mapDamage/mapdamage/python3 mp_test.py

should return

```Started with the command: /usr/local/bin/mapDamage -i tests/test.bam -r tests/fake1.fasta -d tests/results --no-stats Reading from 'tests/test.bam' Writing results to 'tests/results/'pdf tests/results/Fragmisincorporationplot.pdf generatedadditional tests/results/Lengthplot.pdf generatedSuccessful run

.

Ran 2 tests in 3.357s

OK```

Contact

Please report bugs and suggest possible improvements on GitHub:https://github.com/ginolhac/mapDamage/issues/new

wget https://archive.org/download/github.com-ginolhac-mapDamage_-_2021-06-23_07-29-35/ginolhac-mapDamage_-_2021-06-23_07-29-35.bundle

 git clone ginolhac-mapDamage_-_2021-06-23_07-29-35.bundle 

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